A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756855



Internal ID9632314
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:107111363..107167098hg38UCSC Ensembl
Innerchr1:107653985..107709720hg19UCSC Ensembl
Innerchr1:107455508..107511243hg18UCSC Ensembl
Innerchr1:107366027..107421762hg17UCSC Ensembl
Cytoband1p13.3
Allele length
AssemblyAllele length
hg3855736
hg1955736
hg1855736
hg1755736
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758957
Supporting Variantsessv19382, essv24194
SamplesNA07019, NA07056
Known GenesNTNG1
MethodSNP array
AnalysisThe algorithm used to call CNVs using the 500K EA platform was developed to accurately define CNV regions using a large set of reference samples and is described in detail in a separate publication (Komura 2006). The algorithm contains three major parts: 1) Intensity pre-processing using an improved version of Genomic Imbalance Map (GIM) (Ishikawa et al. 2005), including probe selection, noise reduction, normalization, and intensity ratio adjustment based on affinity differences between alleles of a SNP, 2) CNV extraction, which identifies CNVs from all pair-wise comparisons using a modified SW-ARRAY, and 3) A copy number inference step which utilizes signal ratios and SNP information to more precisely define CNV boundaries and the copy number within each region.
PlatformAffymetrix GeneChip Early Access Mapping 500K Set Array (250K_Nsp_SNP)
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2756855
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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